RIN3

Ras and Rab interactor 3, the group of VPS9 domain containing

Basic information

Region (hg38): 14:92513780-92688994

Links

ENSG00000100599 ∙ NCBI:79890 ∙ OMIM:610223 ∙ HGNC:18751 ∙ Uniprot:Q8TB24 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RIN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIN3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			48	6		54
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5			5
Total	0	0	53	7	1

Variants in RIN3

This is a list of pathogenic ClinVar variants found in the RIN3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-92513926-C-A		Squamous cell carcinoma	Uncertain significance (Jun 06, 2022)
14-92514216-AA-TT		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
14-92555756-T-C		not specified	Uncertain significance (May 26, 2024)
14-92555828-A-G		not specified	Uncertain significance (Aug 12, 2022)
14-92555860-A-G		not specified	Likely benign (Jan 23, 2023)
14-92555941-C-T		not specified	Uncertain significance (Jun 05, 2024)
14-92555942-G-A		not specified	Likely benign (Dec 03, 2021)
14-92577388-C-T		not specified	Likely benign (Mar 25, 2024)
14-92577436-C-T		not specified	Uncertain significance (Apr 18, 2023)
14-92577475-C-T		not specified	Uncertain significance (Jun 10, 2024)
14-92577528-A-T		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
14-92615458-T-C		not specified	Uncertain significance (Feb 28, 2024)
14-92641275-A-C		not specified	Uncertain significance (Sep 27, 2022)
14-92641297-C-T		not specified	Uncertain significance (Dec 06, 2022)
14-92641352-G-T		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
14-92641561-A-C		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
14-92651605-C-A		not specified	Uncertain significance (Jul 17, 2023)
14-92651608-C-T		not specified	Uncertain significance (Oct 26, 2022)
14-92651612-A-C		not specified	Uncertain significance (Jun 13, 2022)
14-92651656-G-A		not specified	Uncertain significance (Apr 26, 2023)
14-92651659-T-C		not specified	Uncertain significance (May 27, 2022)
14-92651692-C-T		not specified	Uncertain significance (Sep 01, 2021)
14-92651698-G-A		not specified	Uncertain significance (Jun 06, 2023)
14-92651837-C-T		not specified	Uncertain significance (Jun 17, 2024)
14-92651845-T-A		not specified	Uncertain significance (Jun 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIN3	protein_coding	protein_coding	ENST00000216487	10	175222

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.28e-10	0.939	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.775	555	609	0.912	0.0000381	6324
Missense in Polyphen		165	192.11	0.85887		2003
Synonymous	-0.911	292	273	1.07	0.0000186	2079
Loss of Function	2.00	20	32.2	0.621	0.00000144	390

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000397	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.000277	0.000217
Finnish	0.00106	0.000832
European (Non-Finnish)	0.000310	0.000299
Middle Eastern	0.000277	0.000217
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ras effector protein that functions as a guanine nucleotide exchange (GEF) for RAB5B and RAB31, by exchanging bound GDP for free GTP. Required for normal RAB31 function. {ECO:0000269|PubMed:12972505, ECO:0000269|PubMed:21586568}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.0954

Intolerance Scores

• loftool: 0.446
• rvis_EVS: 0.17
• rvis_percentile_EVS: 64.99

Haploinsufficiency Scores

• pHI: 0.213
• hipred: Y
• hipred_score: 0.565
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.960

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Rin3
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: endocytosis;signal transduction;positive regulation of GTPase activity
• Cellular component: early endosome;cytosol;cytoplasmic vesicle
• Molecular function: GTPase activator activity;protein binding;Rab guanyl-nucleotide exchange factor activity;Rab GTPase binding